Mercurial > repos > chemteam > packmol
comparison template.j2 @ 0:0b8a0ce446f5 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
author | chemteam |
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date | Mon, 08 Oct 2018 05:31:29 -0400 |
parents | |
children | 539fb45630e6 |
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-1:000000000000 | 0:0b8a0ce446f5 |
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1 # Template for packmol in Galaxy | |
2 # | |
3 | |
4 tolerance {{ allparams.tolerance }} | |
5 nloop {{ allparams.nloop }} | |
6 maxit {{ allparams.maxit }} | |
7 seed {{ allparams.seed }} | |
8 filetype {{packmol_format.selected_format}} | |
9 output {{outfile}} | |
10 | |
11 {% for struct in packmol_format.packmol_inputs %} | |
12 structure {{struct.file}} | |
13 # Galaxy datasetname - {{struct.datasetname}} | |
14 number {{struct.structureparams.number}} | |
15 radius {{struct.structureparams.radius}} | |
16 resnumbers {{struct.structureparams.resnumbers}} | |
17 {% for c in struct.structureparams.constraints_repeat %} | |
18 {% if c.constraints.constraint == 'fixed' %} | |
19 {% if c.constraints.center == 'Yes' %} | |
20 center | |
21 {% endif %} | |
22 {{c.constraints.constraint}} {{c.constraints.x}} {{c.constraints.y}} {{c.constraints.z}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.g}} | |
23 {% elif c.constraints.constraint == 'cube' %} | |
24 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.d}} | |
25 {% elif c.constraints.constraint == 'box' %} | |
26 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.xmax}} {{c.constraints.ymax}} {{c.constraints.zmax}} | |
27 {% elif c.constraints.constraint == 'sphere' %} | |
28 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}} | |
29 {% elif c.constraints.constraint == 'ellipsoid' %} | |
30 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} | |
31 {% elif c.constraints.constraint == 'plane' %} | |
32 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}} | |
33 {% elif c.constraints.constraint == 'cylinder' %} | |
34 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} {{c.constraints.l}} | |
35 {% else %} | |
36 unknowntype specified {{c.constraints}} | |
37 {% endif %} | |
38 {% endfor %} | |
39 end structure | |
40 | |
41 {% endfor %} | |
42 |